PFRMAT AL 
TARGET T0085 
AUTHOR 5827-4749-3439 
METHOD Threading alignment for T0085 
METHOD 
METHOD Note: This alignment was edited only by unaligning 
METHOD some portions of the automatic alignment, and by adding 
METHOD the speculation that the N-terminal CXXCH heme-binding motif 
METHOD may occupy nearly the same spatial position as the C-terminal 
METHOD motif of the parent structure. 
METHOD The automatic alignment was: 
METHOD >T0085 Cytochrome C554, Nitrosomonas europaea 
METHOD ADAPFEGRKKCSSCHKAQAQSWKDTAHAKAMESLKPNVKKEAKQKAKLDPAKDYTQDKDCV 
METHOD GCHVDGFGQKGGYTIESPKPMLTGVGCESCHGPGRNFRGDHRKSGQAFEKSGKKTPRKDLA 
METHOD KKGQDFHFEERCSACHLNYE----GSPWKGAKAPYTPFTPEVDAKYTFKFDEMVKEVKAMH 
METHOD EHYKLEGVFEGEPKFKFHDEFQASAKPAKKGK 
METHOD >2cy3__ 
METHOD ADAP-GDDYVISAPEGMKAKPKGDK---------PGALQKTVPFPHTKHA------TVECV 
METHOD QCH-HTLEADGG-----AVK---KCTTSGCHDSLEF-------------RDKANAKDIKLV 
METHOD EN----AFHTQCIDCHKALKKDKKPTGPTACGKCHT--TN--------------------- 
METHOD -------------------------------- 
METHOD 
METHOD This alignment was created by aligning the target sequence to a 
METHOD library of 3D-1D type threading models.  Matching and gap scores 
METHOD were optimized for discriminating remote homolog sequence-structure 
METHOD alignments from alignments on incorrect folds. 
METHOD 
METHOD For this structure template, as well as for other proteins which 
METHOD show significant intermolecular interactions in the PDB file, we 
METHOD calculated two threading models-- one with solvent accessibilities 
METHOD calculated for the domain/chain in isolation, and the other in 
METHOD complex with other domains/chains (or, in this case, with prosthetic 
METHOD groups).  For this target, 2cy3 did NOT 
METHOD score among the best folds.  This is not surprising, since the 
METHOD threading algorithm does not treat the intermolecular protein-heme 
METHOD interactions, which are clearly important for this fold. 
METHOD 
METHOD After HMMs identified the four CXXCH motifs, we constrained the 
METHOD threading alignment to align CH at three positions, but otherwise 
METHOD allowed the alignment to optimize sequence-structure scores for 
METHOD the remaining positions. 
METHOD 
METHOD The three C-terminal CXXCH motifs of the target align to some 
METHOD degree with the three N-terminal motifs of the parent.  When we 
METHOD inspected the structure in 3D, it appeared possible that the  
METHOD N-terminal target motif could occupy roughly the same spatial 
METHOD position as the C-terminal parent motif, so we make this prediction 
METHOD just for fun. 
MODEL 2 
PARENT 2cy3 
C    11    C    111 
S    12    G    112 
S    13    K    113 
C    14    C    114 
H    15    H    115 
D    57    T    41 
K    58    V    42 
D    59    E    43 
C    60    C    44 
V    61    V    45 
G    62    Q    46 
C    63    C    47 
H    64    H    48 
D    66    H    49 
G    67    T    50 
F    68    L    51 
G    69    E    52 
Q    70    A    53 
K    71    D    54 
G    72    G    55 
G    73    G    56 
G    85    K    60 
V    86    C    61 
G    87    T    62 
C    88    T    63 
E    89    S    64 
S    90    G    65 
C    91    C    66 
H    92    H    67 
G    93    D    68 
P    94    S    69 
G    95    L    70 
R    96    E    71 
N    97    F    72 
K    111    R    73 
S    112    D    74 
G    113    K    75 
K    114    A    76 
K    115    N    77 
T    116    A    78 
P    117    K    79 
R    118    D    80 
K    119    I    81 
D    120    K    82 
L    121    L    83 
A    122    V    84 
K    123    E    85 
K    124    N    86 
H    129    A    87 
F    130    F    88 
E    131    H    89 
E    132    T    90 
R    133    Q    91 
C    134    C    92 
S    135    I    93 
A    136    D    94 
C    137    C    95 
H    138    H    96 
L    139    K    97 
N    140    A    98 
Y    141    L    99 
E    142    K    100 
TER 
END 
